Wednesday, June 24, 2009

Nicking transition states from Nick Greeves

Nick Greeves has made a wonderful website called ChemTube3D. And I mean this quite literally, the site is full of wonders: Jmol-animated reaction mechanisms for the most important organic reactions.

I especially like the way the usual 2D representations of reactions are tied to the 3D animation: you click on 2D structures to see 3D structures and "electron pushing", and on arrows to animate the reaction. This really drives home to the point that the static 2D pictures is meant to represent a dynamic 3D model. I wish this has been available when I took organic chemistry, which, somehow, wasn't made any easier by the fact that half the reactions hadn't been discovered yet.

In case you are curious how Nick obtained the structures along the reaction path, you can find the detailed instructions here. Generally speaking, they are obtained by finding the TS of the reaction and then following the atomic forces downhill to reactant and products using the intrinsic reaction coordinate method. This is done in the absence of solvent so for some reactions involving ions there is no barrier (and hence no TS) in the gas phase.

Because Jmol is used, the user can interact with the model, rotate, zoom, measure distances, and access the coordinates! That's right, ChemTube3D is also a transition state (TS) repository, and in the screencast I show how use Avogadro to extract the TS structure. But because the "TS part" of a TS is usually confined to a few bonds, one can use Avogadro to add substituents and create more complex TSs as well.

When I run the input file (which you can find here) that I make at the end of the screencast, GAMESS finds the TS in 20 steps (though I had to remove the $FORCE group which is inserted erroneously by Avogadro).

Finally, Steven Bachrachs blog is another good source for TS structures (many images link to a Jmol display of the structure). Look under the Reactions category in the left-hand column.